PubMed

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs.

Apte AA, Cain JW, Bonchev DG, Fong SS.

J Biol Eng. 2008 Feb 27;2:2.PMID: 18304325 [PubMed - in process]Free PMC ArticleFree textRelated citations

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach.

Ma HW, Buer J, Zeng AP.

BMC Bioinformatics. 2004 Dec 16;5:199.PMID: 15603590 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.

Dobrin R, Beg QK, Barabási AL, Oltvai ZN.

BMC Bioinformatics. 2004 Jan 30;5:10.PMID: 15018656 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Network motifs: structure does not determine function.

Ingram PJ, Stumpf MP, Stark J.

BMC Genomics. 2006 May 5;7:108.PMID: 16677373 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Input-dependent wave propagations in asymmetric cellular automata: possible behaviors of feed-forward loop in biological reaction network.

Awazu A.

Math Biosci Eng. 2008 Jul;5(3):419-27.PMID: 18616349 [PubMed - indexed for MEDLINE]Related citations

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks.

Goemann B, Wingender E, Potapov AP.

BMC Syst Biol. 2009 May 19;3:53.PMID: 19454001 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes.

Ishihara S, Fujimoto K, Shibata T.

Genes Cells. 2005 Nov;10(11):1025-38.PMID: 16236132 [PubMed - indexed for MEDLINE]Related citations

Control of transcriptional variability by overlapping feed-forward regulatory motifs.

Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.

Biophys J. 2008 Oct;95(8):3715-23. Epub 2008 Jul 11.PMID: 18621837 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Comparative analysis of topological patterns in different mammalian networks.

Goemann B, Potapov AP, Ante M, Wingender E.

Genome Inform. 2009 Oct;23(1):32-45.PMID: 20180260 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Stochastic and coherence resonance in feed-forward-loop neuronal network motifs.

Guo D, Li C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 May;79(5 Pt 1):051921. Epub 2009 May 27.PMID: 19518494 [PubMed - indexed for MEDLINE]Related citations

Systems chemistry: logic gates, arithmetic units, and network motifs in small networks.

Wagner N, Ashkenasy G.

Chemistry. 2009;15(7):1765-75.PMID: 19107891 [PubMed - indexed for MEDLINE]Related citations

Subgraphs and network motifs in geometric networks.

Itzkovitz S, Alon U.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 2):026117. Epub 2005 Feb 22.PMID: 15783388 [PubMed]Related citations

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1.PMID: 19426448 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

Kastrup CJ, Runyon MK, Lucchetta EM, Price JM, Ismagilov RF.

Acc Chem Res. 2008 Apr;41(4):549-58. Epub 2008 Jan 25.PMID: 18217723 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

Zhang Q, Bhattacharya S, Andersen ME, Conolly RB.

J Toxicol Environ Health B Crit Rev. 2010 Feb;13(2-4):253-76.PMID: 20574901 [PubMed - in process]Related citations

One hub-one process: a tool based view on regulatory network topology.

Axelsen JB, Bernhardsson S, Sneppen K.

BMC Syst Biol. 2008 Mar 4;2:25.PMID: 18318890 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modular analysis of the transcriptional regulatory network of E. coli.

Resendis-Antonio O, Freyre-González JA, Menchaca-Méndez R, Gutiérrez-Ríos RM, Martínez-Antonio A, Avila-Sánchez C, Collado-Vides J.

Trends Genet. 2005 Jan;21(1):16-20.PMID: 15680508 [PubMed - indexed for MEDLINE]Related citations

Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies.

Knabe JF, Nehaniv CL, Schilstra MJ.

Biosystems. 2008 Oct-Nov;94(1-2):68-74. Epub 2008 Jun 20.PMID: 18611431 [PubMed - indexed for MEDLINE]Related citations

The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.

Mangan S, Itzkovitz S, Zaslaver A, Alon U.

J Mol Biol. 2006 Mar 10;356(5):1073-81. Epub 2005 Dec 19.PMID: 16406067 [PubMed - indexed for MEDLINE]Related citations

Statistical model comparison applied to common network motifs.

Domedel-Puig N, Pournara I, Wernisch L.

BMC Syst Biol. 2010 Mar 3;4:18.PMID: 20199667 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations